[BioC] select one Affy probeset for one gene

[Sean Davis]

On 3/13/06 3:38 PM, "Glazko, Galina" <Galina_Glazko at urmc.rochester.edu>
wrote:

> Dear list,
> 
>  
> 
> Is there a way to automatically select one probeset for one gene in Affy
> arrays? 
> 
> Say, if we have several probesets for a given gene, we select the one
> with the highest level of expression, or based on any other reasonable
> criteria...?
> 
> I am sorry if this question was answered before, it seems to be very
> basic question and I hope there is the solution...

Galina,

You can contrive a solution, I suppose.  However, I'm not sure this is a
good idea.  Whatever "reasonable criteria" you use are likely to lead to
bias.  Filtering on unmeasured probesets or other quality measures applied
equally to all probesets is probably reasonable, but not applying on a
per-gene basis.  There have been related discussions in the past, often
centering around "averaging" expression values.

The more accepted way of dealing with multiple probesets is to do your
analysis based on the probeset; only after that is done do you then connect
your gene labels back to the probesets.

Sean